Dijk, Fien, van (2026) Structural Stability of Self-Replicating GLKFK Hexamer Fibers: A Molecular Dynamics Study. Bachelor's Thesis, Applied Physics.
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Abstract
In this thesis, the structural stability of fibers formed by benzene-1,3-dithiol hexamer macrocycles with GLKFK peptide tails is investigated using all-atom molecular dynamics simulations. The GLKFK hexameric macrocycle is a self-replicating peptide system in which fiber formation drives exponential replication, making fiber stability directly relevant to self-replication mechanism. Four fiber systems were studied: cartwheel and pairwise geometric arrangements, each simulated with and without position restraints on the carbon alpha atoms between consecutive layers of the fiber, resulting in four 100 ns trajectories. Structural properties including backbone hydrogen bonds, interlayer spacing, ring plane angles, beta-sheet content, chloride ion association and radial water- and ion- density were calculated and compared across all four systems.
| Item Type: | Thesis (Bachelor's Thesis) |
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| Supervisor name: | Dibajeh, A.J.F. |
| Degree programme: | Applied Physics |
| Thesis type: | Bachelor's Thesis |
| Language: | English |
| Date Deposited: | 09 Apr 2026 13:59 |
| Last Modified: | 09 Apr 2026 13:59 |
| URI: | https://fse.studenttheses.ub.rug.nl/id/eprint/37279 |
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